Re: [AMBER] Antechamber trouble with COA-acyl chain

From: David A Case <>
Date: Tue, 12 Jul 2011 14:43:34 -0400

On Tue, Jul 12, 2011, Erin Kelly wrote:

> Here is the most recent pdb.
> > > I've been trying to produce a mol2 file from a pdb generated using
> > ChemDraw

This pdb file is seriously flawed, and has so many problems I hardly know
where to begin :-)

1. Atoms 30 and 32 are almost on top of one another
2. All the phosphates are protonated (probably not what you want for anything
    near physiological conditions.
3. Oxygen atom 10 is less than 1 Ang from a neighboring nitrogen.
4. The adenine ring is highly reduced and is virtually unrecognizable.

Even with a good starting structure, this molecule would be a challenge: the
am1-bcc prescription requires a (local) minimum at the AM1 level, which will
take a while to find for such a big molecule. It probably could be made
to work (be patient) if you had a good starting structure, but you might want
to consider building this molecule in pieces.


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Received on Tue Jul 12 2011 - 12:00:03 PDT
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